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dof_manager_default.cc
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			/**
			* @file dof_manager_default.cc
			*
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			*
			* @date creation: Tue Aug 18 2015
			* @date last modification: Thu Feb 08 2018
			*
			* @brief Implementation of the default DOFManager
			*
			*
			* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
			* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
			*
			* Akantu is free software: you can redistribute it and/or modify it under the
			* terms of the GNU Lesser General Public License as published by the Free
			* Software Foundation, either version 3 of the License, or (at your option) any
			* later version.
			*
			* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
			* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
			* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
			* details.
			*
			* You should have received a copy of the GNU Lesser General Public License
			* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
			*
			*/

			/* -------------------------------------------------------------------------- */
			#include "dof_manager_default.hh"
			#include "communicator.hh"
			#include "dof_synchronizer.hh"
			#include "element_group.hh"
			#include "non_linear_solver_default.hh"
			#include "periodic_node_synchronizer.hh"
			#include "solver_vector_default.hh"
			#include "solver_vector_distributed.hh"
			#include "sparse_matrix_aij.hh"
			#include "time_step_solver_default.hh"

			/* -------------------------------------------------------------------------- */
			#include <algorithm>
			#include <memory>
			#include <numeric>
			#include <unordered_map>
			/* -------------------------------------------------------------------------- */

			namespace akantu {

			/* -------------------------------------------------------------------------- */
			DOFManagerDefault::DOFManagerDefault(const ID & id)
			: DOFManager(id), synchronizer(nullptr) {
			residual = std::make_unique<SolverVectorDefault>(
			*this, std::string(id + ":residual"));
			solution = std::make_unique<SolverVectorDefault>(
			*this, std::string(id + ":solution"));
			data_cache = std::make_unique<SolverVectorDefault>(
			*this, std::string(id + ":data_cache"));
			}

			/* -------------------------------------------------------------------------- */
			DOFManagerDefault::DOFManagerDefault(Mesh & mesh, const ID & id)
			: DOFManager(mesh, id), synchronizer(nullptr) {
			if (this->mesh->isDistributed()) {
			this->synchronizer = std::make_unique<DOFSynchronizer>(
			*this, this->id + ":dof_synchronizer");
			residual = std::make_unique<SolverVectorDistributed>(
			*this, std::string(id + ":residual"));
			solution = std::make_unique<SolverVectorDistributed>(
			*this, std::string(id + ":solution"));
			data_cache = std::make_unique<SolverVectorDistributed>(
			*this, std::string(id + ":data_cache"));

			} else {
			residual = std::make_unique<SolverVectorDefault>(
			*this, std::string(id + ":residual"));
			solution = std::make_unique<SolverVectorDefault>(
			*this, std::string(id + ":solution"));
			data_cache = std::make_unique<SolverVectorDefault>(
			*this, std::string(id + ":data_cache"));
			}
			}

			/* -------------------------------------------------------------------------- */
			DOFManagerDefault::~DOFManagerDefault() = default;

			/* -------------------------------------------------------------------------- */
			void DOFManagerDefault::makeConsistentForPeriodicity(const ID & dof_id,
			SolverVector & array) {
			auto & dof_data = this->getDOFDataTyped<DOFDataDefault>(dof_id);
			if (dof_data.support_type != _dst_nodal) {
			return;
			}

			if (not mesh->isPeriodic()) {
			return;
			}

			this->mesh->getPeriodicNodeSynchronizer()
			.reduceSynchronizeWithPBCSlaves<AddOperation>(
			aka::as_type<SolverVectorDefault>(array).getVector());
			}

			/* -------------------------------------------------------------------------- */
			template <typename T>
			void DOFManagerDefault::assembleToGlobalArray(
			const ID & dof_id, const Array<T> & array_to_assemble,
			Array<T> & global_array, T scale_factor) {
			AKANTU_DEBUG_IN();

			auto & dof_data = this->getDOFDataTyped<DOFDataDefault>(dof_id);
			AKANTU_DEBUG_ASSERT(dof_data.local_equation_number.size() ==
			array_to_assemble.size() *
			array_to_assemble.getNbComponent(),
			"The array to assemble does not have a correct size."
			<< " (" << array_to_assemble.getID() << ")");

			if (dof_data.support_type == _dst_nodal and mesh->isPeriodic()) {
			for (auto && data :
			zip(dof_data.local_equation_number, dof_data.associated_nodes,
			make_view(array_to_assemble))) {
			auto && equ_num = std::get<0>(data);
			// auto && node = std::get<1>(data);
			auto && arr = std::get<2>(data);

			// Guillaume to Nico:
			// This filter of periodic slave should not be.
			// Indeed you want to get the contribution even
			// from periodic slaves and cumulate to the right
			// equation number.

			global_array(equ_num) += scale_factor * (arr);
			// scale_factor * (arr) * (not this->mesh->isPeriodicSlave(node));
			}
			} else {
			for (auto && data :
			zip(dof_data.local_equation_number, make_view(array_to_assemble))) {
			auto && equ_num = std::get<0>(data);
			auto && arr = std::get<1>(data);
			global_array(equ_num) += scale_factor * (arr);
			}
			}
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void DOFManagerDefault::assembleToGlobalArray(
			const ID & dof_id, const Array<Real> & array_to_assemble,
			SolverVector & global_array_v, Real scale_factor) {

			assembleToGlobalArray(
			dof_id, array_to_assemble,
			aka::as_type<SolverVectorDefault>(global_array_v).getVector(),
			scale_factor);
			}

			/* -------------------------------------------------------------------------- */
			DOFManagerDefault::DOFDataDefault::DOFDataDefault(const ID & dof_id)
			: DOFData(dof_id) {}

			/* -------------------------------------------------------------------------- */
			auto DOFManagerDefault::getNewDOFData(const ID & dof_id)
			-> std::unique_ptr<DOFData> {
			return std::make_unique<DOFDataDefault>(dof_id);
			}

			/* -------------------------------------------------------------------------- */
			std::tuple<UInt, UInt, UInt>
			DOFManagerDefault::registerDOFsInternal(const ID & dof_id,
			Array<Real> & dofs_array) {
			auto ret = DOFManager::registerDOFsInternal(dof_id, dofs_array);

			// update the synchronizer if needed
			if (this->synchronizer) {
			this->synchronizer->registerDOFs(dof_id);
			}

			return ret;
			}

			/* -------------------------------------------------------------------------- */
			SparseMatrix & DOFManagerDefault::getNewMatrix(const ID & id,
			const MatrixType & matrix_type) {
			return this->registerSparseMatrix<SparseMatrixAIJ>(*this, id, matrix_type);
			}

			/* -------------------------------------------------------------------------- */
			SparseMatrix & DOFManagerDefault::getNewMatrix(const ID & id,
			const ID & matrix_to_copy_id) {
			return this->registerSparseMatrix<SparseMatrixAIJ>(id, matrix_to_copy_id);
			}

			/* -------------------------------------------------------------------------- */
			SolverVector & DOFManagerDefault::getNewLumpedMatrix(const ID & id) {
			return this->registerLumpedMatrix<SolverVectorDefault>(*this, id);
			}

			/* -------------------------------------------------------------------------- */
			SparseMatrixAIJ & DOFManagerDefault::getMatrix(const ID & id) {
			auto & matrix = DOFManager::getMatrix(id);
			return aka::as_type<SparseMatrixAIJ>(matrix);
			}

			/* -------------------------------------------------------------------------- */
			NonLinearSolver &
			DOFManagerDefault::getNewNonLinearSolver(const ID & id,
			const NonLinearSolverType & type) {
			switch (type) {
			#if defined(AKANTU_USE_MUMPS)
			case NonLinearSolverType::_newton_raphson:
			/* FALLTHRU */
			/* [[fallthrough]]; un-comment when compiler will get it */
			case NonLinearSolverType::_newton_raphson_modified: {
			return this->registerNonLinearSolver<NonLinearSolverNewtonRaphson>(
			*this, id, type);
			}
			case NonLinearSolverType::_linear: {
			return this->registerNonLinearSolver<NonLinearSolverLinear>(*this, id,
			type);
			}
			#endif
			case NonLinearSolverType::_lumped: {
			return this->registerNonLinearSolver<NonLinearSolverLumped>(*this, id,
			type);
			}
			default:
			AKANTU_EXCEPTION("The asked type of non linear solver is not supported by "
			"this dof manager");
			}
			}

			/* -------------------------------------------------------------------------- */
			TimeStepSolver & DOFManagerDefault::getNewTimeStepSolver(
			const ID & id, const TimeStepSolverType & type,
			NonLinearSolver & non_linear_solver, SolverCallback & solver_callback) {
			return this->registerTimeStepSolver<TimeStepSolverDefault>(
			*this, id, type, non_linear_solver, solver_callback);
			}

			/* -------------------------------------------------------------------------- */
			template <typename T>
			void DOFManagerDefault::getArrayPerDOFs(const ID & dof_id,
			const Array<T> & global_array,
			Array<T> & local_array) const {
			AKANTU_DEBUG_IN();

			const Array<Int> & equation_number = this->getLocalEquationsNumbers(dof_id);

			UInt nb_degree_of_freedoms = equation_number.size();
			local_array.resize(nb_degree_of_freedoms / local_array.getNbComponent());

			auto loc_it = local_array.begin_reinterpret(nb_degree_of_freedoms);
			auto equ_it = equation_number.begin();

			for (UInt d = 0; d < nb_degree_of_freedoms; ++d, ++loc_it, ++equ_it) {
			(loc_it) = global_array(equ_it);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void DOFManagerDefault::getArrayPerDOFs(const ID & dof_id,
			const SolverVector & global_array,
			Array<Real> & local_array) {
			getArrayPerDOFs(dof_id,
			aka::as_type<SolverVectorDefault>(global_array).getVector(),
			local_array);
			}

			/* -------------------------------------------------------------------------- */
			void DOFManagerDefault::assembleLumpedMatMulVectToResidual(
			const ID & dof_id, const ID & A_id, const Array<Real> & x,
			Real scale_factor) {
			const Array<Real> & A = this->getLumpedMatrix(A_id);
			auto & cache = aka::as_type<SolverVectorArray>(*this->data_cache);

			cache.zero();
			this->assembleToGlobalArray(dof_id, x, cache.getVector(), scale_factor);

			for (auto && data : zip(make_view(A), make_view(cache.getVector()),
			make_view(this->getResidualArray()))) {
			const auto & A = std::get<0>(data);
			const auto & x = std::get<1>(data);
			auto & r = std::get<2>(data);
			r += A * x;
			}
			}

			/* -------------------------------------------------------------------------- */
			void DOFManagerDefault::assembleElementalMatricesToMatrix(
			const ID & matrix_id, const ID & dof_id, const Array<Real> & elementary_mat,
			ElementType type, GhostType ghost_type,
			const MatrixType & elemental_matrix_type,
			const Array<UInt> & filter_elements) {
			this->addToProfile(matrix_id, dof_id, type, ghost_type);
			auto & A = getMatrix(matrix_id);
			DOFManager::assembleElementalMatricesToMatrix_(
			A, dof_id, elementary_mat, type, ghost_type, elemental_matrix_type,
			filter_elements);
			}

			/* -------------------------------------------------------------------------- */
			void DOFManagerDefault::assemblePreassembledMatrix(
			const ID & dof_id_m, const ID & dof_id_n, const ID & matrix_id,
			const TermsToAssemble & terms) {
			auto & A = getMatrix(matrix_id);
			DOFManager::assemblePreassembledMatrix_(A, dof_id_m, dof_id_n, terms);
			}

			/* -------------------------------------------------------------------------- */
			void DOFManagerDefault::assembleMatMulVectToArray(const ID & dof_id,
			const ID & A_id,
			const Array<Real> & x,
			Array<Real> & array,
			Real scale_factor) {
			if (mesh->isDistributed()) {
			DOFManager::assembleMatMulVectToArray_<SolverVectorDistributed>(
			dof_id, A_id, x, array, scale_factor);
			} else {
			DOFManager::assembleMatMulVectToArray_<SolverVectorDefault>(
			dof_id, A_id, x, array, scale_factor);
			}
			}

			/* -------------------------------------------------------------------------- */
			void DOFManagerDefault::addToProfile(const ID & matrix_id, const ID & dof_id,
			ElementType type, GhostType ghost_type) {
			AKANTU_DEBUG_IN();

			const auto & dof_data = this->getDOFData(dof_id);

			if (dof_data.support_type != _dst_nodal) {
			return;
			}

			auto mat_dof = std::make_pair(matrix_id, dof_id);
			auto type_pair = std::make_pair(type, ghost_type);

			auto prof_it = this->matrix_profiled_dofs.find(mat_dof);
			if (prof_it != this->matrix_profiled_dofs.end() &&
			std::find(prof_it->second.begin(), prof_it->second.end(), type_pair) !=
			prof_it->second.end()) {
			return;
			}

			auto nb_degree_of_freedom_per_node = dof_data.dof->getNbComponent();

			const auto & equation_number = this->getLocalEquationsNumbers(dof_id);

			auto & A = this->getMatrix(matrix_id);
			A.resize(system_size);
			auto size = A.size();

			auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);

			const auto & connectivity = this->mesh->getConnectivity(type, ghost_type);
			auto cbegin = connectivity.begin(nb_nodes_per_element);
			auto cit = cbegin;

			auto nb_elements = connectivity.size();
			UInt * ge_it = nullptr;
			if (dof_data.group_support != "__mesh__") {
			const auto & group_elements =
			this->mesh->getElementGroup(dof_data.group_support)
			.getElements(type, ghost_type);
			ge_it = group_elements.storage();
			nb_elements = group_elements.size();
			}

			UInt size_mat = nb_nodes_per_element * nb_degree_of_freedom_per_node;
			Vector<Int> element_eq_nb(size_mat);

			for (UInt e = 0; e < nb_elements; ++e) {
			if (ge_it != nullptr) {
			cit = cbegin + *ge_it;
			}

			this->extractElementEquationNumber(
			equation_number, *cit, nb_degree_of_freedom_per_node, element_eq_nb);
			std::transform(
			element_eq_nb.storage(), element_eq_nb.storage() + element_eq_nb.size(),
			element_eq_nb.storage(),
			[&](auto & local) { return this->localToGlobalEquationNumber(local); });

			if (ge_it != nullptr) {
			++ge_it;
			} else {
			++cit;
			}

			for (UInt i = 0; i < size_mat; ++i) {
			UInt c_irn = element_eq_nb(i);
			if (c_irn < size) {
			for (UInt j = 0; j < size_mat; ++j) {
			UInt c_jcn = element_eq_nb(j);
			if (c_jcn < size) {
			A.add(c_irn, c_jcn);
			}
			}
			}
			}
			}

			this->matrix_profiled_dofs[mat_dof].push_back(type_pair);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			Array<Real> & DOFManagerDefault::getSolutionArray() {
			return dynamic_cast<SolverVectorDefault *>(this->solution.get())->getVector();
			}

			/* -------------------------------------------------------------------------- */
			const Array<Real> & DOFManagerDefault::getResidualArray() const {
			return dynamic_cast<SolverVectorDefault *>(this->residual.get())->getVector();
			}

			/* -------------------------------------------------------------------------- */
			Array<Real> & DOFManagerDefault::getResidualArray() {
			return dynamic_cast<SolverVectorDefault *>(this->residual.get())->getVector();
			}

			/* -------------------------------------------------------------------------- */
			void DOFManagerDefault::onNodesAdded(const Array<UInt> & nodes_list,
			const NewNodesEvent & event) {
			DOFManager::onNodesAdded(nodes_list, event);

			if (this->synchronizer) {
			this->synchronizer->onNodesAdded(nodes_list);
			}
			}

			/* -------------------------------------------------------------------------- */
			void DOFManagerDefault::resizeGlobalArrays() {
			DOFManager::resizeGlobalArrays();

			this->global_blocked_dofs.resize(this->local_system_size, 1);
			this->previous_global_blocked_dofs.resize(this->local_system_size, 1);

			matrix_profiled_dofs.clear();
			}

			/* -------------------------------------------------------------------------- */
			void DOFManagerDefault::updateGlobalBlockedDofs() {
			DOFManager::updateGlobalBlockedDofs();

			if (this->global_blocked_dofs_release ==
			this->previous_global_blocked_dofs_release) {
			return;
			}

			global_blocked_dofs_uint.resize(local_system_size);
			global_blocked_dofs_uint.set(false);
			for (const auto & dof : global_blocked_dofs) {
			global_blocked_dofs_uint[dof] = true;
			}
			}

			/* -------------------------------------------------------------------------- */
			Array<bool> & DOFManagerDefault::getBlockedDOFs() {
			return global_blocked_dofs_uint;
			}

			/* -------------------------------------------------------------------------- */
			const Array<bool> & DOFManagerDefault::getBlockedDOFs() const {
			return global_blocked_dofs_uint;
			}

			/* -------------------------------------------------------------------------- */
			static bool dof_manager_is_registered [[gnu::unused]] =
			DOFManagerFactory::getInstance().registerAllocator(
			"default",
			[](Mesh & mesh, const ID & id) -> std::unique_ptr<DOFManager> {
			return std::make_unique<DOFManagerDefault>(mesh, id);
			});

			static bool dof_manager_is_registered_mumps [[gnu::unused]] =
			DOFManagerFactory::getInstance().registerAllocator(
			"mumps",
			[](Mesh & mesh, const ID & id) -> std::unique_ptr<DOFManager> {
			return std::make_unique<DOFManagerDefault>(mesh, id);
			});

			} // namespace akantu

rAKA/src/model/common/dof_manager/dof_manager_default.cc33327d9f46e4bugfixes/41-group-not…

dof_manager_default.ccView Options

rAKA/src/model/common/dof_manager/dof_manager_default.cc
33327d9f46e4bugfixes/41-group-not…

dof_manager_default.cc
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